CETN3

gene
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Also known as CEN3

Summary

CETN3 (centrin 3, HGNC:1868) is a protein-coding gene on chromosome 5q14.3, encoding Centrin-3 (O15182). Plays a fundamental role in microtubule-organizing center structure and function.

The protein encoded by this gene contains four EF-hand calcium binding domains, and is a member of the centrin protein family. Centrins are evolutionarily conserved proteins similar to the CDC31 protein of S. cerevisiae. Yeast CDC31 is located at the centrosome of interphase and mitotic cells, where it plays a fundamental role in centrosome duplication and separation. Multiple forms of the proteins similar to the yeast centrin have been identified in human and other mammalian cells, some of which have been shown to be associated with centrosome fractions. This protein appears to be one of the most abundant centrins associated with centrosome, which suggests a similar function to its yeast counterpart. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 1070 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 22 total
  • MANE Select transcript: NM_004365

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1868
Approved symbolCETN3
Namecentrin 3
Location5q14.3
Locus typegene with protein product
StatusApproved
AliasesCEN3
Ensembl geneENSG00000153140
Ensembl biotypeprotein_coding
OMIM602907
Entrez1070

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 14 protein_coding, 1 nonsense_mediated_decay

ENST00000283122, ENST00000518458, ENST00000522083, ENST00000522565, ENST00000522842, ENST00000522864, ENST00000909756, ENST00000909757, ENST00000919887, ENST00000919888, ENST00000919889, ENST00000919890, ENST00000919891, ENST00000919892, ENST00000919893

RefSeq mRNA: 3 — MANE Select: NM_004365 NM_001297765, NM_001297768, NM_004365

CCDS: CCDS4066, CCDS75274, CCDS78036

Canonical transcript exons

ENST00000283122 — 5 exons

ExonStartEnd
ENSE000010090409040964590409756
ENSE000010090419040568590405799
ENSE000010090439040769990407834
ENSE000012665309039225790394107
ENSE000036668489039935890399549

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 99.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.5221 / max 1085.4831, expressed in 1790 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
6252131.66791785
625180.4760266
625200.3782139

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002399.09gold quality
adult organismUBERON:000702398.82gold quality
left testisUBERON:000453398.77gold quality
right testisUBERON:000453498.77gold quality
testisUBERON:000047397.66gold quality
secondary oocyteCL:000065597.40gold quality
bronchial epithelial cellCL:000232897.35gold quality
palpebral conjunctivaUBERON:000181296.98gold quality
germinal epithelium of ovaryUBERON:000130496.84gold quality
ventricular zoneUBERON:000305396.57gold quality
calcaneal tendonUBERON:000370196.32gold quality
spermCL:000001996.29gold quality
amniotic fluidUBERON:000017395.88gold quality
epithelium of bronchusUBERON:000203195.85gold quality
male germ cellCL:000001595.81gold quality
parietal pleuraUBERON:000240095.57gold quality
mucosa of paranasal sinusUBERON:000503095.57gold quality
bronchusUBERON:000218595.53gold quality
pigmented layer of retinaUBERON:000178295.51gold quality
embryoUBERON:000092295.46gold quality
ganglionic eminenceUBERON:000402395.22gold quality
pleuraUBERON:000097795.01gold quality
visceral pleuraUBERON:000240194.87gold quality
endometriumUBERON:000129594.81gold quality
esophagus squamous epitheliumUBERON:000692094.59gold quality
caput epididymisUBERON:000435894.40gold quality
epithelium of nasopharynxUBERON:000195194.19gold quality
corpus epididymisUBERON:000435994.04gold quality
seminal vesicleUBERON:000099893.98gold quality
corpus callosumUBERON:000233693.91gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting CETN3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3163100.0077.238605
HSA-MIR-4673100.0066.641490
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-365899.9673.874379
HSA-MIR-651-3P99.9473.485177
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-576-5P99.8470.462582
HSA-MIR-548AZ-5P99.8369.943230
HSA-MIR-548T-5P99.8369.913220
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-313399.8170.923506
HSA-MIR-129999.7771.242389
HSA-MIR-199A-3P99.7570.48929
HSA-MIR-199B-3P99.7570.48929
HSA-MIR-3129-5P99.7570.46914
HSA-MIR-1212499.6869.172700
HSA-MIR-651-5P99.6468.491104
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-875-3P99.6369.472548
HSA-MIR-426999.5569.891373
HSA-MIR-392399.5269.21446
HSA-MIR-203A-3P99.4970.562806

Literature-anchored findings (GeneRIF, showing 2)

  • could be classified as a Ca(2+) sensor protein (PMID:15654740)
  • Cetn3 inhibits Mps1 autophosphorylation at Thr-676, a known site of T-loop autoactivation, and interferes with Mps1-dependent phosphorylation of Cetn2. The cellular overexpression of Cetn3 attenuates the incorporation of Cetn2 into centrioles and centrosome reduplication, whereas depletion of Cetn3 generates extra centrioles. (PMID:26354417)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriocetn3ENSDARG00000011825
mus_musculusCetn3ENSMUSG00000021537
rattus_norvegicusCetn3ENSRNOG00000050877
drosophila_melanogasterTpnC4FBGN0033027
caenorhabditis_elegansWBGENE00000285
caenorhabditis_elegansWBGENE00000287
caenorhabditis_eleganspat-10WBGENE00003934
caenorhabditis_elegansWBGENE00006583
caenorhabditis_elegansWBGENE00008453
caenorhabditis_elegansF35C12.3WBGENE00009408
caenorhabditis_elegansWBGENE00015264

Paralogs (20): CABP7 (ENSG00000100314), CABP5 (ENSG00000105507), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CABP2 (ENSG00000167791), CALML6 (ENSG00000169885), EFCAB3 (ENSG00000172421), EFCAB12 (ENSG00000172771), CABP4 (ENSG00000175544), CETN1 (ENSG00000177143), CALML3 (ENSG00000178363), CALML5 (ENSG00000178372), CALN1 (ENSG00000183166), CALM1 (ENSG00000198668), EFCAB2 (ENSG00000203666), EFCAB7 (ENSG00000203965), EFCAB9 (ENSG00000214360)

Protein

Protein identifiers

Centrin-3O15182 (reviewed: O15182)

All UniProt accessions (6): O15182, E5RFM2, E5RH67, E5RJF8, E5RK82, H0YBL5

UniProt curated annotations — full annotation on UniProt →

Function. Plays a fundamental role in microtubule-organizing center structure and function. As a component of the TREX-2 complex, involved in the export of mRNAs to the cytoplasm through the nuclear pores.

Subunit / interactions. Monomer. Component of the nuclear pore complex (NPC)-associated TREX-2 complex (transcription and export complex 2), composed of at least GANP, 2 copies of ENY2, PCID2, SEM1/DSS1, and either centrin CETN2 or centrin CETN3. The TREX-2 complex also associates with ALYREF/ALY and with the nucleoporin NUP153. Interacts with USP49.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Nucleus. Nucleolus. Nucleus envelope. Nuclear pore complex. Centriole.

Similarity. Belongs to the centrin family.

RefSeq proteins (3): NP_001284694, NP_001284697, NP_004356* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002048EF_hand_domDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR050230CALM/Myosin/TropC-likeFamily

Pfam: PF13499

UniProt features (12 total): binding site 5, domain 4, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15182-F188.950.79

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (5): 147; 149; 151; 153; 158

Post-translational modifications (1): 135

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 202 (showing top): PAL_PRMT5_TARGETS_UP, MORF_BRCA1, MORF_ATRX, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, KAUFFMANN_DNA_REPAIR_GENES, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_NUCLEAR_TRANSPORT, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, MORF_PPP5C, GOCC_CENTROSOME, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP

GO Biological Process (5): microtubule cytoskeleton organization (GO:0000226), centrosome cycle (GO:0007098), protein transport (GO:0015031), mRNA transport (GO:0051028), cell division (GO:0051301)

GO Molecular Function (5): calcium ion binding (GO:0005509), microtubule binding (GO:0008017), G-protein beta/gamma-subunit complex binding (GO:0031683), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (14): nucleolus (GO:0005730), centrosome (GO:0005813), centriole (GO:0005814), microtubule organizing center (GO:0005815), photoreceptor connecting cilium (GO:0032391), ciliary basal body (GO:0036064), nuclear pore nuclear basket (GO:0044615), transcription export complex 2 (GO:0070390), nucleus (GO:0005634), nuclear envelope (GO:0005635), nuclear pore (GO:0005643), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), ciliary transition zone (GO:0035869)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle3
microtubule organizing center3
cellular anatomical structure3
nuclear protein-containing complex3
cilium2
cytoskeleton organization1
microtubule-based process1
cell cycle process1
microtubule organizing center organization1
transport1
intracellular protein localization1
establishment of protein localization1
RNA transport1
cellular process1
metal ion binding1
tubulin binding1
protein-containing complex binding1
binding1
cation binding1
nuclear lumen1
centriole1
microtubule cytoskeleton1
ciliary transition zone1
photoreceptor cell cilium1
nuclear pore1
intracellular membrane-bounded organelle1
nucleus1
endomembrane system1
organelle envelope1
nuclear envelope1
intracellular anatomical structure1

Protein interactions and networks

STRING

3223 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CETN3SFI1A8K8P3914
CETN3MCM3APO60318899
CETN3ENY2Q9NPA8899
CETN3PCID2Q5JVF3864
CETN3SASS6Q6UVJ0699
CETN3FBXL13Q8NEE6680
CETN3RPS4XP12631640
CETN3PHKA1P46020638
CETN3SEM1Q6ZVN7635
CETN3POC5Q8NA72624
CETN3CEP164Q9UPV0622
CETN3CEP63Q96MT8617
CETN3PCNTO95613614
CETN3PLK4O00444606
CETN3CEP135Q66GS9604
CETN3CENPAP49450604

IntAct

136 interactions, top by confidence:

ABTypeScore
ZWINTNDC80psi-mi:“MI:0914”(association)0.940
POC5CETN3psi-mi:“MI:0915”(physical association)0.920
CETN3POC5psi-mi:“MI:0915”(physical association)0.920
POC5CETN3psi-mi:“MI:0914”(association)0.920
CETN3POC5psi-mi:“MI:0915”(physical association)0.770
POC5CETN3psi-mi:“MI:0914”(association)0.770
CETN2SFI1psi-mi:“MI:0914”(association)0.740
XPCCETN3psi-mi:“MI:0914”(association)0.730
CETN3SGSM1psi-mi:“MI:0915”(physical association)0.720
SGSM1CETN3psi-mi:“MI:0915”(physical association)0.720
CETN1SFI1psi-mi:“MI:0914”(association)0.640
RHODPLXNB2psi-mi:“MI:0914”(association)0.640
BCKDKCETN3psi-mi:“MI:0914”(association)0.640
DCAF12L2CETN3psi-mi:“MI:0914”(association)0.640

BioGRID (111): SGSM1 (Two-hybrid), POC5 (Two-hybrid), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), CETN3 (Two-hybrid), CETN3 (Proximity Label-MS), CETN3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS)

ESM2 similar proteins: A0A125YHX7, A0A125YZN2, J9W034, O15182, O23184, O35648, O74435, O82659, P02597, P02599, P04352, P05434, P05933, P06704, P27163, P27164, P27482, P41041, P41208, P41209, P41210, P43645, P43646, P49258, P53440, P53441, P54213, P60204, P60205, P60206, P61859, P61860, P61861, Q06827, Q12798, Q24956, Q27177, Q27178, Q27179, Q2TBN3

Diamond homologs: A0A125YHX7, A0A125YZN2, A2WN93, A2WNH1, A2Y609, A3E3H0, A3E4D8, A3E4F9, A4UHC0, A8CEP3, A8I1Q0, J9W034, O15182, O23184, O35648, O60041, O74435, O82018, O82659, O94739, O96102, P02597, P02598, P04352, P04353, P04464, P05419, P05434, P06704, P06787, P07463, P0DH95, P0DH96, P0DH97, P0DH98, P11120, P11121, P13868, P15094, P17928

SIGNOR signaling

2 interactions.

AEffectBMechanism
CCP110“up-regulates activity”CETN3binding
PCM1up-regulatesCETN3relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 89 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Loss of Nlp from mitotic centrosomes513.9×4e-03
Loss of proteins required for interphase microtubule organization from the centrosome513.9×4e-03
AURKA Activation by TPX2513.4×4e-03
Recruitment of mitotic centrosome proteins and complexes511.9×5e-03
Regulation of PLK1 Activity at G2/M Transition511.1×6e-03
Recruitment of NuMA to mitotic centrosomes510.2×8e-03
Anchoring of the basal body to the plasma membrane59.9×8e-03

GO biological processes:

GO termPartnersFoldFDR
centriole replication657.1×2e-07
regulation of cytokinesis738.3×2e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

22 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance15
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1010 predictions. Top by Δscore:

VariantEffectΔscore
5:90394108:C:CCacceptor_gain1.0000
5:90399356:A:ACdonor_gain1.0000
5:90399357:C:CCdonor_gain1.0000
5:90399357:CTTT:Cdonor_gain1.0000
5:90399545:TGTCA:Tacceptor_gain1.0000
5:90399547:TCA:Tacceptor_gain1.0000
5:90399548:CA:Cacceptor_gain1.0000
5:90399548:CAC:Cacceptor_gain1.0000
5:90399550:C:CCacceptor_gain1.0000
5:90405680:CACA:Cdonor_loss1.0000
5:90405682:CACC:Cdonor_loss1.0000
5:90405683:A:ACdonor_gain1.0000
5:90405684:C:CCdonor_gain1.0000
5:90405684:C:CTdonor_loss1.0000
5:90405684:CCAA:Cdonor_gain1.0000
5:90405687:A:ACdonor_gain1.0000
5:90405688:C:CCdonor_gain1.0000
5:90405690:T:TAdonor_gain1.0000
5:90405795:GCCAC:Gacceptor_gain1.0000
5:90405796:CCAC:Cacceptor_gain1.0000
5:90405796:CCACC:Cacceptor_gain1.0000
5:90405797:CACC:Cacceptor_gain1.0000
5:90405799:CCTT:Cacceptor_loss1.0000
5:90405799:CCTTT:Cacceptor_gain1.0000
5:90405801:T:Aacceptor_loss1.0000
5:90405801:T:Cacceptor_gain1.0000
5:90405801:T:TCacceptor_gain1.0000
5:90405803:T:Cacceptor_gain1.0000
5:90405803:T:TCacceptor_gain1.0000
5:90405808:T:Cacceptor_gain1.0000

AlphaMissense

1134 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:90405780:C:TG58E1.000
5:90405781:C:AG58W1.000
5:90394091:G:CF159L0.999
5:90394091:G:TF159L0.999
5:90394092:A:GF159S0.999
5:90394093:A:GF159L0.999
5:90399402:A:GL139P0.999
5:90399438:G:TA127D0.999
5:90399439:C:GA127P0.999
5:90399441:A:TV126D0.999
5:90399444:C:GR125P0.999
5:90399450:A:GL123S0.999
5:90399465:A:CI118R0.999
5:90399465:A:GI118T0.999
5:90399465:A:TI118K0.999
5:90399488:A:CF110L0.999
5:90399488:A:TF110L0.999
5:90399490:A:GF110L0.999
5:90399492:A:GL109P0.999
5:90399497:A:CF107L0.999
5:90399497:A:TF107L0.999
5:90399498:A:GF107S0.999
5:90399499:A:GF107L0.999
5:90405696:A:GF86S0.999
5:90405780:C:AG58V0.999
5:90405781:C:GG58R0.999
5:90405781:C:TG58R0.999
5:90405795:G:TA53E0.999
5:90405796:C:GA53P0.999
5:90407745:A:GL36P0.999

dbSNP variants (sampled 300 via entrez): RS1000037514 (5:90393268 C>G), RS1000156640 (5:90400739 G>A), RS1000223089 (5:90408463 A>G,T), RS1000434154 (5:90397271 A>G), RS1000455198 (5:90397576 T>C), RS1000527948 (5:90406351 T>C), RS1000638146 (5:90391813 G>A), RS1000733844 (5:90401217 G>C), RS1000756068 (5:90398945 A>G), RS1001161121 (5:90400569 T>C), RS1001345871 (5:90393295 C>T), RS1001555780 (5:90396746 A>C), RS1001592001 (5:90397102 C>T), RS1001783143 (5:90408059 C>A), RS1001798760 (5:90400283 A>C)

Disease associations

OMIM: gene MIM:602907 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST000478_3Type 2 diabetes7.000000e-07
GCST005790_49Rosacea symptom severity7.000000e-06
GCST90011900_56Serum alkaline phosphatase levels4.000000e-17

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0009180rosacea severity measurement
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
potassium chromate(VI)affects cotreatment, decreases expression2
Air Pollutantsaffects cotreatment, increases abundance, increases expression, decreases expression2
Ethanolaffects cotreatment, increases abundance, decreases expression2
Valproic Acidincreases expression, affects expression, decreases methylation2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamideincreases expression1
GSK-J4decreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases expression, increases abundance, affects cotreatment1
arseniteincreases reaction, affects binding1
methylparabenaffects splicing, increases expression1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression1
azoxystrobinincreases expression1
CGP 52608affects binding, increases reaction1
deguelindecreases expression1
bisphenol Sincreases expression, affects cotreatment1
Rosiglitazonedecreases expression1
Decitabineaffects expression1
Acroleinincreases expression, increases abundance, affects cotreatment1
Antimycin Adecreases expression1
Cisplatinaffects expression1
Dexamethasoneaffects cotreatment, increases expression1
Estradioldecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.